The Library Manager is a graphical user interface for administrating monomers in the libraries accessed by the Biomolecule Toolkit and BioEddie.
The Biomolecule Toolkit operates with a monomer library that is persisted in its own database schema. This library is typically shared across multiple users and labeled as „Remote”.
BioEddie can operate with the remote library as well as with a „Local” library that resides in the browser cache. The local library is unique to a given browser sessions and cannot be shared with others.
When configured accordingly for BioEddie, switching between local and remote library is possible by clicking on the library selection drop-down
Selecting a monomer of the library will display a secondary panel showing the full data of a monomer. Modifications to a monomer can be applied here, while actions to add, delete, or duplicate are available from the main monomer table.
Monomers can be filtered based on partial and full matches in the following fields
Matches in their additional data (attribute, value)
Add a new monomer
Select a monomer type in the dropdown
If PEPTIDE, CHEM or RNA monomer type is selected, then chemical structure can be defined for the monomer. Click on to open Marvin JS and create the monomer structure with R-groups
Define the Name, Abbreviation and the Natural Analogue for the new monomer
Select the leaving groups for the corresponding R-groups in the drop-downs
Provide additional data if required by clicking on ’Add new’. If the remote library is selected, click on the empty additional data field and select from the registered monomer additional data. Additional data attributes and corresponding values can be removed by clicking on
Click on Save
The Biomolecule Toolkit uses a controlled list of attributes, hence registering monomers with custom additional data attributes will require you to add these to the controlled list prior to registering monomers using these.
The local library does not exhibit that restriction. Here any additional data attribute can be added for the monomers without restriction.
Hover over a monomer to be deleted
Click on and delete the monomer
The separate monomer libraries (local and remote) can be exported and downloaded in JSON by clicking on ’Export’ on the Library Manager interface.
Monomer in JSON format can be imported to the local library by clicking on ’Import’ on the interface and selecting the corresponding JSON file.